When I first started playing Pokémon, I theorized that Poké balls only worked on pokémon who shared certain genetic traits. In theory, Chao are close enough to pokémon, and maybe the aliens are too, but it has no effect on humans. Basically what I'm trying to get at here, is that Chaos basically just crammed Red in there.

Actually, in the episode where they met that Mankey, the Mankey threw a rice ball at Ash when he tried to catch him. And for lack of a better word, Ash caught the rice ball. So a Pokéball could probably catch a human.

I saw this great commercial on Kids WB (back when they had Pokemon), where Ash actually gets sucked into a Poke Ball. Inside is where the strange Kids WB 'sock dude' lives, and Ash finds all of his missing socks in there [a mountain of them], and the sock dude says, "Well... I was lonely."